Yes. You can use either HM Revenue & Customs (HMRC) software or commercial software to submit the Company Tax Return online even if your accounting period has changed.
If you use HMRC's software, you can change the accounting period that's shown, or tell HMRC about a new one, by following the ‘File a return and accounts’ on-screen prompts. You can then download and complete the HMRC online filing software for the changed accounting period.
If you use commercial software, you can provide the accounting period start and end dates as part of the return and, depending on your software package, the software may enter this for you automatically.
Whichever software you use, your accounting period (the return period) can't be more than 12 months long but it may be shorter depending on your company's circumstances. If your accounts are for a period of more than 12 months long please see the FAQ 'My accounts are for a period of more than 12 months. How can I file a Company Tax Return?'